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The New Zealand champion of the past three years, John Derry, of Blenheim, will defend his lead against Dale Whiteside, of Alberta, Canada, who lies in second place and fellow New Zealander Ben Baxter, of Winton, who is third overall.
They are among 39 teams from Canada, Mexico and New Zealand.
Race organiser Tim Guthrie, of Mosgiel, yesterday said the marathon had been troubled by a few mechanical failures, which was just a part of racing, but also by ''appalling'' weather.
''We cancelled leg eight on the Waiau River [on Monday afternoon] for safety reasons because of torrential rain, high winds, river rising into flood and poor visibility ... to make sure everybody got off the river safe.''
However, Mr Guthrie predicted the Dart River would be in good shape for drivers to race the 35km from the Glenorchy boat ramp up to Beans Burn, with as many as 14 boats on the water at one time.
The marathon crews will tackle the Matukituki and Clutha rivers tomorrow. A prizegiving will be at the Golden Gate Lodge, Cromwell, on Friday night.
Mr Guthrie described the event as ''a huge economy boost'' for Otago and Southland. An estimated $75,000 to $100,000 is spent daily by teams.
The marathon is sanctioned by the New Zealand Jet Boat River Racing Association, the New Zealand Power Boat Federation and the Union Internationale Motonautique, with the support of the Otago Branch and Southland Branch of Jet Boating New Zealand.